Centre for Philosophy of Science Applied Evolutionary Epistemology Lab

Luís Villarreal

introducing the virus-first and collective perspective, acknowledgment of the contributions of many.
Limitation of our large social brain: anchored and linear thinking

Day-by-Day Program

Lecture 1: An Overview of Concepts to be Integrated into Subsequent Topics

Virome influence on life from pre-LUCA to human. Virus defined and debated. Virus as 'agents' not elements. The nature of 'variation' from virus. Early chemical and 'fittest individual type' concepts (Manfred Eigen) for the origin of code: the importance of quasispecies. Experimental evaluation of quasispecies establishes a cooperative or consortial nature. A redefinition of quasispecies: QS-C as cooperative. Clear distinctions with Fisher population genetics: Survival of the mob. Belong to the mob; group identity and network membership. Defectives as effectives. The persistence of code.

  1. Villarreal, Luis P. Viruses and the Evolution of Life. ASM Press, 2005.
  2. Villarreal, Luis P. Origin of Group Identity: Viruses, Addiction and Cooperation. Springer, 2008.
  3. Carrapiço, Francisco. "How Symbiogenic is Eevolution?" Theory in Biosciences 129.2 (2010): 135-139.
  4. Ryan, Frank P. "Genomic Creativity and Natural Selection: a Modern Synthesis." Biological Journal of the Linnean Society 88.4 (2006): 655-672.
  5. Shelton, Deborah E., and Richard E. Michod. "Philosophical Foundations for the Hierarchy of Life." Biology and Philosophy 25.3 (2010): 391-403.

 

Lecture 2: Stem-loop RNA and the Origin of Virus and LUCA: Collective and Infectious Beginnings

Stem-loop RNA as precellular life. Invasive, preclusive, competing and complementing replicators. Replicator (group identity) and cooperative RNA. RNA stem loops: the origin of viroids and virus. The role of amino acids in replicator priming and identity. Reconsider tRNA as replicator identity and the origin of symbolic code. The need for consortia, minority types and memory of past experience. Membrane enclosed identity, the collective origin of the ribosomes (stem-loops). How 7 S RNA/RNP can provide membrane enclosed identity.

 

Lecture 3: Prokaryotes: Islands of Immunity in an Infectious Sea. The Immense and Ancient DNA Virome

Did virus invent DNA and capture RNA societies? Horizontal transfer or virome colonization? The great 'gene centric' exchange by virus. Defectives and transposons. Viral persistence mechanisms defines addiction modules. The need to kill in order to save. Viral origins of immunity. Sensing other groups and killing them. The exemplar of toxigenic E. coli: collective action of mixed and defective phage. Phage and photosynthesis: origin of toxic O2 and photosynthesis. The extended genotype: integrated virus and host identity. Biofilms, cryptic prophage and toxins.

 

Lecture 4: Eukaryotes: The Great Retrovirus (Poson) Colonization and the Creation of Regulatory Complexity

A major shift in virus-host dynmics. Multiple (cooperative) identity (multicellularity) mediated by virus addiction and symbiosis Why gene numbers don't account for complexity. Did virus invent the nucleus? A separation that allows identity modification (RNA editing, epigenetics and translational control). Viral origins of epigenetics. The viral source of regulatory networks. C. elegans as the exemplar: LTRs, ERVs and transmissible RNAi. Stem-loop RNA still matters for identity. Slugs and bugs (parasitoids), some amazing examples of virus mediated symbiosis. How to engineer a host for live birth.

 

Lecture 5: Mammals: the Placents, Vivipary and Social Bonding. Another Great ERV Colonization, Cooperating with TEs

Viral colonization and mammalian development: how to reprogram everything. A parasitic, invasive and defective egg: the origin of the placenta. Virus mediated formation of the complex and diffuse placental network. The adaptive immune system and virus. Motherhood as a social addiction module: role of the placenta. Learning to mother: olfaction, VNO and the MHC locus. Behavior and the enlarged brain: the role of addiction centers. Virus modulation of social (pair) bonding; insights into creating social networks.

 

Suggested Further Reading

The following specific references are roughly in order of presentation:

Villarreal, Luis P. "Are viruses alive?." SCIENTIFIC AMERICAN-AMERICAN EDITION- 291 (2004): 100-105.

Witzany, Günther. "Natural genome-editing competences of viruses." Acta biotheoretica 54.4 (2006): 235-253.

WITZANY, Gnther. "Viruses: essential agents of life." (2012).

Forterre, Patrick. "Defining life: the virus viewpoint." Origins of Life and Evolution of Biospheres 40.2 (2010): 151-160.

Jalasvuori, Matti, and Jaana KH Bamford. "Viruses and Life: Can There Be One Without the Other." Journal of Cosmology 10 (2010): 3446-3454.

Jalasvuori, Matti, and Jaana KH Bamford. "Structural co-evolution of viruses and cells in the primordial world." Origins of Life and Evolution of Biospheres 38.2 (2008): 165-181.

Fisher, Susie. "Are RNA Viruses Vestiges of an RNA World?." Darwinism, Philosophy, and Experimental Biology (2011): 67-87.

Domingo, E., et al. "Viruses as quasispecies: biological implications." Quasispecies: Concept and Implications for Virology (2006): 51-82.

Holmes, Bob. "First life may have survived by cooperating." New Scientist 216.2887 (2012): 10.

Domingo, Esteban, and John J. Holland. The origin and evolution of viruses. John Wiley & Sons, Ltd, 2005.

Lauring, Adam S., and Raul Andino. "Quasispecies theory and the behavior of RNA viruses." PLoS pathogens 6.7 (2010): e1001005.

Arbiza, Juan, Santiago Mirazo, and Hugo Fort. "Viral quasispecies profiles as the result of the interplay of competition and cooperation." BMC evolutionary biology 10.1 (2010): 137.

Ojosnegros, Samuel, et al. "Quasispecies as a matter of fact: Viruses and beyond." Virus research (2011).

Attwater, James, and Philipp Holliger. "Origins of life: The cooperative gene." Nature 491.7422 (2012): 48-49.

Arenas, Carolina Díaz, and Niles Lehman. "Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube." BMC evolutionary biology 10.1 (2010): 80.

RNA networks:  Dadon, Zehavit, et al. "Reaction Networks." Supramolecular Chemistry: From Molecules to Nanomaterials (2012).

Vaidya, Nilesh, et al. "Spontaneous network formation among cooperative RNA replicators." Nature (2012).

Hordijk, Wim, and Mike Steel. "A formal model of autocatalytic sets emerging in an RNA replicator system." arXiv preprint arXiv:1211.3473 (2012).

Szathmáry, Eörs. "On the propagation of a conceptual error concerning hypercycles and cooperation." Journal of Systems Chemistry 4.1 (2013): 1.

Jalasvuori, Matti, Maija P. Jalasvuori, and Jaana KH Bamford. "Dynamics of a laterally evolving community of ribozyme-like agents as studied with a rule-based computing system." Origins of Life and Evolution of Biospheres 40.3 (2010): 319-334.

Harish, Ajith, and Gustavo Caetano-Anollés. "Ribosomal history reveals origins of modern protein synthesis." PloS one 7.3 (2012): e32776.

Transition to the DNA world: 

Villarreal, Luis P. "The Addiction Module as a Social Force." Viruses: Essential Agents of Life. Springer Netherlands, 2012. 107-145.

Villarreal, Luis P. "How viruses shape the tree of life." Future Virology 1.5 (2006): 587-595.

Villarreal, Luis P. "Persistence pays: how viruses promote host group survival." Current opinion in microbiology 12.4 (2009): 467-472.

Witzany, Günther. "Natural Genome Editing Competences of Viruses and Virus-Like Agents." Biocommunication and Natural Genome Editing. Springer Netherlands, 2010. 129-147.

Koonin, Eugene V., and Yuri I. Wolf. "Evolution of microbes and viruses: a paradigm shift in evolutionary biology?." Frontiers in Cellular and Infection Microbiology 2 (2012).

Abroi, Aare, and Julian Gough. "Are viruses a source of new protein folds for organisms?–Virosphere structure space and evolution."Bioessays 33.8 (2011): 626-635.

Diemer, Geoffrey, and Kenneth Stedman. "A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses." Biology direct 7.1 (2012): 13.

Claverie, Jean-Michel. "Virus evolution: From neglect to center stage, amidst some confusion." Preprint Archive, Quantitative Biology: 1-12.

Filée, Jonathan, Patrick Forterre, and Jacqueline Laurent. "The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies." Research in microbiology 154.4 (2003): 237-243.

Forterre, Patrick. "The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells." Biochimie 87.9 (2005): 793-803.

Claverie, Jean-Michel. "Viruses take center stage in cellular evolution." Genome Biol 7.6 (2006): 110.

RNA viruses and plants:

Roossinck, Marilyn J. "Lifestyles of plant viruses." Philosophical Transactions of the Royal Society B: Biological Sciences 365.1548 (2010): 1899-1905.

Roossinck, Marilyn J. "Symbiosis, mutualism and symbiogenesis." Evolution of plant virus. Springer, Berlin (2008): 157-164.

Roossinck, Marilyn J. "The good viruses: viral mutualistic symbioses." Nature Reviews Microbiology 9.2 (2011): 99-108.

Virus and host immunity:

Villarreal, Luis P. "The Source of Self." Annals of the New York Academy of Sciences 1178.1 (2009): 194-232.

Villarreal, Luis P. "Viral ancestors of antiviral systems." Viruses 3.10 (2011): 1933-1958.

Webb, Bruce A., et al. "Polydnavirus genomes reflect their dual roles as mutualists and pathogens." Virology 347.1 (2006): 160-174.

Parasites that manipulate social insect behavior: 

Villarreal, Luis P., and L. P. Villareal. "On viruses, sex, and motherhood." Journal of virology 71.2 (1997): 859.

Varela, Mariana, et al. "Friendly Viruses." Annals of the New York Academy of Sciences 1178.1 (2009): 157-172.

Kidwell, Margaret G., and Damon R. Lisch. "Perspective: transposable elements, parasitic DNA, and genome evolution." Evolution 55.1 (2001): 1-24.

Villarreal, Luis P. "Can viruses make us human?." Proceedings of the American Philosophical Society (2004): 296-323.

Van Blerkom, Linda M. "Role of viruses in human evolution." American journal of physical anthropology 122.S37 (2003): 14-46.

Ryan, Frank P. "Human endogenous retroviruses in health and disease: a symbiotic perspective." JRSM 97.12 (2004): 560-565.

 

Additional References